Downstram Analysis of the results of the Deconvolution

1.- Clustering based on cell abundances

Low Resolution = 0.25 (Few clusters)

Higher Resolution = 0.75 (More clusters)

We save the results to compute the Neigborhod enrichment analysis in the following script.

2.- Proportions of all the cell types per sample-

3-. Identify groups of co-located cell types using matrix factorisation

From Cell2Location tutorial: Tip If you want to find a few most disctinct cellular compartments, use a small number of factors. If you want to find very strong co-location signal and assume that most cell types don’t co-locate, use a lot of factors (> 30 - used here). In practice, it is better to train NMF for a range of factors R=5,..,30 and select R as a balance between capturing fine tissue zones and splitting known compartments

R = 5

R = 10

R = 15

R = 20